Author: "Guillaume Achaz" - Searchworks@Jio Institute Digital Library Search Results

Your search keyword '"Guillaume Achaz"' showing total 89 results

Start Over Author "Guillaume Achaz"

89 results on '"Guillaume Achaz"'

1. Evo‐Scope: Fully automated assessment of correlated evolution on phylogenetic trees

Author: Maxime Godfroid, Charles Coluzzi, Amaury Lambert, Philippe Glaser, Eduardo P. C. Rocha, and Guillaume Achaz
Subjects: correlated evolution, phylogenetics, workflow, Ecology, QH540-549.5, Evolution, QH359-425
Abstract: Abstract Correlated evolution describes how multiple biological traits evolve together. Recently developed methods provide increasingly detailed results of correlated evolution, sometimes at elevated computational costs. Here, we present evo‐scope, a fast and fully automated pipeline with minimal input requirements to compute correlation between discrete traits evolving on a phylogenetic tree. Notably, we improve two of our previously developed tools that efficiently compute statistics of correlated evolution to characterize the nature, such as synergy or antagonism, and the strength of the interdependence between the traits. Furthermore, we improved the running time and implemented several additional features, such as genetic mapping, Bayesian Markov Chain Monte Carlo estimation, consideration of missing data and phylogenetic uncertainty. As an application, we scan a publicly available penicillin resistance data set of Streptococcus pneumoniae and characterize genetic mutations that correlate with antibiotic resistance. The pipeline is accessible both as a self‐contained Github repository (https://github.com/Maxime5G/EvoScope) and through a graphical galaxy interface (https://galaxy.pasteur.fr/u/maximeg/w/evoscope).
Published: 2024
Full Text: View/download PDF

2. CNCA aligns small annotated genomes

Author: Jean-Noël Lorenzi, François Graner, Virginie Courtier-Orgogozo, and Guillaume Achaz
Subjects: Annotated genomes, Nucleotide alignment, Protein alignment, Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5
Abstract: Abstract Background To explore the evolutionary history of sequences, a sequence alignment is a first and necessary step, and its quality is crucial. In the context of the study of the proximal origins of SARS-CoV-2 coronavirus, we wanted to construct an alignment of genomes closely related to SARS-CoV-2 using both coding and non-coding sequences. To our knowledge, there is no tool that can be used to construct this type of alignment, which motivated the creation of CNCA. Results CNCA is a web tool that aligns annotated genomes from GenBank files. It generates a nucleotide alignment that is then updated based on the protein sequence alignment. The output final nucleotide alignment matches the protein alignment and guarantees no frameshift. CNCA was designed to align closely related small genome sequences up to 50 kb (typically viruses) for which the gene order is conserved. Conclusions CNCA constructs multiple alignments of small genomes by integrating both coding and non-coding sequences. This preserves regions traditionally ignored in conventional back-translation methods, such as non-coding regions.
Published: 2024
Full Text: View/download PDF

3. The Crown Pearl V2: an improved genome assembly of the European freshwater pearl mussel Margaritifera margaritifera (Linnaeus, 1758)

Author: André Gomes-dos-Santos, Manuel Lopes-Lima, André M. Machado, Thomas Forest, Guillaume Achaz, Amílcar Teixeira, Vincent Prié, L. Filipe C. Castro, and Elsa Froufe
Subjects: Electronic computers. Computer science, QA75.5-76.95
Abstract: Contiguous assemblies are fundamental to deciphering the composition of extant genomes. In molluscs, this is considerably challenging owing to the large size of their genomes, heterozygosity, and widespread repetitive content. Consequently, long-read sequencing technologies are fundamental for high contiguity and quality. The first genome assembly of Margaritifera margaritifera (Linnaeus, 1758) (Mollusca: Bivalvia: Unionida), a culturally relevant, widespread, and highly threatened species of freshwater mussels, was recently generated. However, the resulting genome is highly fragmented since the assembly relied on short-read approaches. Here, an improved reference genome assembly was generated using a combination of PacBio CLR long reads and Illumina paired-end short reads. This genome assembly is 2.4 Gb long, organized into 1,700 scaffolds with a contig N50 length of 3.4 Mbp. The ab initio gene prediction resulted in 48,314 protein-coding genes. Our new assembly is a substantial improvement and an essential resource for studying this species’ unique biological and evolutionary features, helping promote its conservation.
Published: 2023
Full Text: View/download PDF

4. Interpreting the pervasive observation of U-shaped Site Frequency Spectra.

Author: Fabian Freund, Elise Kerdoncuff, Sebastian Matuszewski, Marguerite Lapierre, Marcel Hildebrandt, Jeffrey D Jensen, Luca Ferretti, Amaury Lambert, Timothy B Sackton, and Guillaume Achaz
Subjects: Genetics, QH426-470
Abstract: The standard neutral model of molecular evolution has traditionally been used as the null model for population genomics. We gathered a collection of 45 genome-wide site frequency spectra from a diverse set of species, most of which display an excess of low and high frequency variants compared to the expectation of the standard neutral model, resulting in U-shaped spectra. We show that multiple merger coalescent models often provide a better fit to these observations than the standard Kingman coalescent. Hence, in many circumstances these under-utilized models may serve as the more appropriate reference for genomic analyses. We further discuss the underlying evolutionary processes that may result in the widespread U-shape of frequency spectra.
Published: 2023
Full Text: View/download PDF

5. Involvement of ADGRV1 Gene in Familial Forms of Genetic Generalized Epilepsy

Author: Maha Dahawi, Mohamed S. Elmagzoub, Elhami A. Ahmed, Sara Baldassari, Guillaume Achaz, Fatima A. Elmugadam, Wasma A. Abdelgadir, Stéphanie Baulac, Julien Buratti, Omer Abdalla, Sahar Gamil, Maha Alzubeir, Rayan Abubaker, Eric Noé, Liena Elsayed, Ammar E. Ahmed, and Eric Leguern
Subjects: ADGRV1, genetic generalized epilepsy, absence epilepsy, susceptibility gene, oligogenism, Neurology. Diseases of the nervous system, RC346-429
Abstract: Background: Genetic generalized epilepsies (GGE) including childhood absence epilepsy (CAE), juvenile absence epilepsy (JAE), juvenile myoclonic epilepsy (JME), and GGE with tonic–clonic seizures alone (GGE-TCS), are common types of epilepsy mostly determined by a polygenic mode of inheritance. Recent studies showed that susceptibility genes for GGE are numerous, and their variants rare, challenging their identification. In this study, we aimed to assess GGE genetic etiology in a Sudanese population.Methods: We performed whole-exome sequencing (WES) on DNA of 40 patients from 20 Sudanese families with GGE searching for candidate susceptibility variants, which were prioritized by CADD software and functional features of the corresponding gene. We assessed their segregation in 138 individuals and performed genotype–phenotype correlations.Results: In a family including three sibs with GGE-TCS, we identified a rare missense variant in ADGRV1 encoding an adhesion G protein-coupled receptor V1, which was already involved in the autosomal recessive Usher type C syndrome. In addition, five other ADGRV1 rare missense variants were identified in four additional families and absent from 119 Sudanese controls. In one of these families, an ADGRV1 variant was found at a homozygous state, in a female more severely affected than her heterozygous brother, suggesting a gene dosage effect. In the five families, GGE phenotype was statistically associated with ADGRV1 variants (0R = 0.9 103).Conclusion: This study highly supports, for the first time, the involvement of ADGRV1 missense variants in familial GGE and that ADGRV1 is a susceptibility gene for CAE/JAE and GGE-TCS phenotypes.
Published: 2021
Full Text: View/download PDF

6. Is reproductive strategy a key factor in understanding the evolutionary history of Southern Ocean Asteroidea (Echinodermata)?

Author: Camille Moreau, Bruno Danis, Quentin Jossart, Marc Eléaume, Chester Sands, Guillaume Achaz, Antonio Agüera, and Thomas Saucède
Subjects: Antarctica, Asteroidea, bipolarity, brooding, Echinodermata, emergence, Ecology, QH540-549.5
Abstract: Abstract Life traits such as reproductive strategy can be determining factors of species evolutionary history and explain the resulting diversity patterns. This can be investigated using phylogeographic analyses of genetic units. In this work, the genetic structure of five asteroid genera with contrasting reproductive strategies (brooding: Diplasterias, Notasterias and Lysasterias versus broadcasting: Psilaster and Bathybiaster) was investigated in the Southern Ocean. Over 1,400 mtDNA cytochrome C oxidase subunit I (COI) sequences were analysed using five species delineation methods (ABGD, ASAP, mPTP, sGMYC and mGMYC), two phylogenetic reconstructions (ML and BA), and molecular clock calibrations, in order to examine the weight of reproductive strategy in the observed differences among phylogeographic patterns. We hypothesised that brooding species would show higher levels of genetic diversity and species richness along with a clearer geographic structuring than broadcasting species. In contrast, genetic diversity and species richness were not found to be significantly different between brooders and broadcasters, but broadcasters are less spatially structured than brooders supporting our initial hypothesis and suggesting more complex evolutionary histories associated to this reproductive strategy. Broadcasters' phylogeography can be explained by different scenarios including deep‐sea colonisation routes, bipolarity or cosmopolitanism, and sub‐Antarctic emergence for the genus Bathybiaster; Antarctic‐ New Zealand faunal exchanges across the Polar Front for the genus Psilaster. Brooders' phylogeography could support the previously formulated hypothesis of a past trans‐Antarctic seaway established between the Ross and the Weddell seas during the Plio‐Pleistocene. Our results also show, for the first time, that the Weddell Sea is populated by a mixed asteroid fauna originating from both the East and West Antarctic.
Published: 2019
Full Text: View/download PDF

7. Quiescence unveils a novel mutational force in fission yeast

Author: Serge Gangloff, Guillaume Achaz, Stefania Francesconi, Adrien Villain, Samia Miled, Claire Denis, and Benoit Arcangioli
Subjects: molecular clock, evolution, mutations, stem cells, postmitotic, Medicine, Science, Biology (General), QH301-705.5
Abstract: To maintain life across a fluctuating environment, cells alternate between phases of cell division and quiescence. During cell division, the spontaneous mutation rate is expressed as the probability of mutations per generation (Luria and Delbrück, 1943; Lea and Coulson, 1949), whereas during quiescence it will be expressed per unit of time. In this study, we report that during quiescence, the unicellular haploid fission yeast accumulates mutations as a linear function of time. The novel mutational landscape of quiescence is characterized by insertion/deletion (indels) accumulating as fast as single nucleotide variants (SNVs), and elevated amounts of deletions. When we extended the study to 3 months of quiescence, we confirmed the replication-independent mutational spectrum at the whole-genome level of a clonally aged population and uncovered phenotypic variations that subject the cells to natural selection. Thus, our results support the idea that genomes continuously evolve under two alternating phases that will impact on their size and composition.
Published: 2017
Full Text: View/download PDF

8. Towards a genetic theory of island biogeography: Inferring processes from multidimensional community‐scale data

Author: Isaac, Overcast, Guillaume, Achaz, Robin, Aguilée, Carmelo, Andújar, Paula, Arribas, Thomas J., Creedy, Evan P., Economo, Rampal S., Etienne, Rosemary, Gillespie, Claire, Jacquet, Flora, Jay, Susan, Kennedy, Henrik, Krehenwinkel, Amaury, Lambert, Emmanouil, Meramveliotakis, Víctor, Noguerales, Benoit, Perez‐Lamarque, George, Roderick, Haldre, Rogers, Megan, Ruffley, Isabel, Sanmartin, Alfried P., Vogler, Anna, Papadopoulou, Brent C., Emerson, Hélène, Morlon, Isaac, Overcast, Guillaume, Achaz, Robin, Aguilée, Carmelo, Andújar, Paula, Arribas, Thomas J., Creedy, Evan P., Economo, Rampal S., Etienne, Rosemary, Gillespie, Claire, Jacquet, Flora, Jay, Susan, Kennedy, Henrik, Krehenwinkel, Amaury, Lambert, Emmanouil, Meramveliotakis, Víctor, Noguerales, Benoit, Perez‐Lamarque, George, Roderick, Haldre, Rogers, Megan, Ruffley, Isabel, Sanmartin, Alfried P., Vogler, Anna, Papadopoulou, Brent C., Emerson, and Hélène, Morlon
Abstract: BackgroundMacArthur and Wilson's theory of island biogeography has been a foundation for obtaining testable predictions from models of community assembly and for developing models that integrate across scales and disciplines. Historically, however, these developments have focused on integration across ecological and macroevolutionary scales and on predicting patterns of species richness, abundance distributions, trait data and/or phylogenies. The distribution of genetic variation across species within a community is an emerging pattern that contains signatures of past population histories, which might provide an historical lens for the study of contemporary communities. As intraspecific genetic diversity data become increasingly available at the scale of entire communities, there is an opportunity to integrate microevolutionary processes into our models, moving towards development of a genetic theory of island biogeography.Motivation/goalWe aim to promote the development of process-based biodiversity models that predict community genetic diversity patterns together with other community-scale patterns. To this end, we review models of ecological, microevolutionary and macroevolutionary processes that are best suited to the creation of unified models, and the patterns that these predict. We then discuss ongoing and potential future efforts to unify models operating at different organizational levels, with the goal of predicting multidimensional community-scale data including a genetic component.Main conclusionsOur review of the literature shows that despite recent efforts, further methodological developments are needed, not only to incorporate the genetic component into existing island biogeography models, but also to unify processes across scales of biological organization. To catalyse these developments, we outline two potential ways forward, adopting either a top-down or a bottom-up approach. Finally, we highlight key ecological and evolutionary questions that migh, source:https://onlinelibrary.wiley.com/doi/10.1111/geb.13604
Published: 2023

9. Cultural transmission of reproductive success impacts genomic diversity, coalescent tree topologies, and demographic inferences

Author: Jérémy Guez, Guillaume Achaz, François Bienvenu, Jean Cury, Bruno Toupance, Évelyne Heyer, Flora Jay, Frédéric Austerlitz, Éco-Anthropologie (EA), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), BioInformatique (BioInfo), Laboratoire Interdisciplinaire des Sciences du Numérique (LISN), Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Science des Données (SDD), Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Centre interdisciplinaire de recherche en biologie (CIRB), Labex MemoLife, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Collège de France (CdF (institution))-Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), TAckling the Underspecified (TAU), Inria Saclay - Ile de France, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire Interdisciplinaire des Sciences du Numérique (LISN), Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-CentraleSupélec-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Evolution et ingénierie de systèmes dynamiques (SEED (UMR-S 1284/U 1284)), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité), Bioinformatique (LRI) (BioInfo - LRI), Laboratoire de Recherche en Informatique (LRI), CentraleSupélec-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-CentraleSupélec-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), ANR-20-CE45-0010,RoDAPoG,Apprentissage profond robuste pour la génomique des populations(2020), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Jay, Flora, and Apprentissage profond robuste pour la génomique des populations - - RoDAPoG2020 - ANR-20-CE45-0010 - AAPG2020 - VALID
Subjects: coalescent tree shape, Genetics, population genetics, genetic diversity, [SDV.BID]Life Sciences [q-bio]/Biodiversity, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], demographic inference, imbalanced topology, cultural process, [SDV.BID] Life Sciences [q-bio]/Biodiversity, [INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM]
Abstract: Cultural transmission of reproductive success has been observed in many human populations as well as other animals. Cultural transmission of reproductive success consists of a positive correlation of nongenetic origin between the progeny size of parents and children. This correlation can result from various factors, such as the social influence of parents on their children, the increase of children’s survival through allocare from uncles and aunts, or the transmission of resources. Here, we study the evolution of genomic diversity over time under cultural transmission of reproductive success. Cultural transmission of reproductive success has a threefold impact on population genetics: (1) the effective population size decreases when cultural transmission of reproductive success starts, mimicking a population contraction, and increases back to its original value when cultural transmission of reproductive success stops; (2) coalescent tree topologies are distorted under cultural transmission of reproductive success, with higher imbalance and a higher number of polytomies; and (3) branch lengths are reduced nonhomogenously, with a higher impact on older branches. Under long-lasting cultural transmission of reproductive success, the effective population size stabilizes but the distortion of tree topology and the nonhomogenous branch length reduction remain, yielding U-shaped site frequency spectra under a constant population size. We show that this yields a bias in site frequency spectra-based demographic inference. Considering that cultural transmission of reproductive success was detected in numerous human and animal populations worldwide, one should be cautious because inferring population past histories from genomic data can be biased by this cultural process.
Published: 2023
Full Text: View/download PDF

10. The Crown Pearl V2: an improved genome assembly of the European freshwater pearl musselMargaritifera margaritifera(Linnaeus, 1758)

Author: André Gomes-dos-Santos, Manuel Lopes-Lima, André M. Machado, Thomas Forest, Guillaume Achaz, Amílcar Teixeira, Vincent Prié, L. Filipe C. Castro, and Elsa Froufe
Abstract: Contiguous assemblies are fundamental to decipher the exact composition of extant genomes. In molluscs, this task is considerably challenging owing to their large size, heterozygosity, and widespread content of repetitive content. Consequently, the usage of long-read sequencing technologies is fundamental to achieve high contiguity and quality. The first genome assembly ofMargaritifera margaritifera(Linnaeus, 1758) (Mollusca: Bivalvia: Unionida), a culturally relevant, widespread, and highly threatened species of freshwater mussels, has been produced recently. However, the current genome is highly fragmented since the assembly relied solely on short-read approaches. To overcome this caveat, here, a new improved reference genome assembly is produced using a combination of PacBio CLR long reads and Illumina paired-end short reads. This novel genome assembly is 2.4 Gb long, organized into 1,700 scaffolds with a contig N50 length of 3.4Mbp. Theab initiogene prediction resulted in a total of 48,314 protein-coding genes. This new assembly represents a substantial improvement and is an essential resource for studying this species’ unique biological and evolutionary features that ultimately will help to promote its conservation.
Published: 2023
Full Text: View/download PDF

11. A Minimal yet Flexible Likelihood Framework to Assess Correlated Evolution

Author: Joël Pothier, Amaury Lambert, Guillaume Achaz, Patrice Petot, Abdelkader Behdenna, and Maxime Godfroid
Subjects: Likelihood Functions, Sequence, Mutation rate, Models, Genetic, Phylogenetic tree, Estimation theory, Model selection, Sample (statistics), Biology, Biological Evolution, Evolution, Molecular, Phenotype, RNA, Ribosomal, 16S, Genetics, Trait, Algorithm, Phylogeny, Ecology, Evolution, Behavior and Systematics, Independence (probability theory)
Abstract: An evolutionary process is reflected in the sequence of changes of any trait (e.g., morphological or molecular) through time. Yet, a better understanding of evolution would be procured by characterizing correlated evolution, or when two or more evolutionary processes interact. Previously developed parametric methods often require significant computing time as they rely on the estimation of many parameters. Here, we propose a minimal likelihood framework modeling the joint evolution of two traits on a known phylogenetic tree. The type and strength of correlated evolution are characterized by a few parameters tuning mutation rates of each trait and interdependencies between these rates. The framework can be applied to study any discrete trait or character ranging from nucleotide substitution to gain or loss of a biological function. More specifically, it can be used to 1) test for independence between two evolutionary processes, 2) identify the type of interaction between them, and 3) estimate parameter values of the most likely model of interaction. In the current implementation, the method takes as input a phylogenetic tree with discrete evolutionary events mapped on its branches. The method then maximizes the likelihood for one or several chosen scenarios. The strengths and limits of the method, as well as its relative power compared to a few other methods, are assessed using both simulations and data from 16S rRNA sequences in a sample of 54 $\gamma$-enterobacteria. We show that, even with data sets of fewer than 100 species, the method performs well in parameter estimation and in evolutionary model selection. [Correlated evolution; maximum likelihood; model.]
Published: 2021
Full Text: View/download PDF

12. Evo-Scope: Fully automated assessment of correlated evolution on phylogenetic trees

Author: Maxime Godfroid, Charles Coluzzi, Amaury Lambert, Philippe Glaser, Eduardo P. C. Rocha, and Guillaume Achaz
Abstract: Correlated evolution describes how multiple biological traits evolve together. Recently developed methods provide increasingly detailed results of correlated evolution, sometimes at elevated computational costs.Here, we presentevo-scope, a fast and fully-automated pipeline with minimal input requirements to compute correlation between discrete traits evolving on a phylogenetic tree. Notably, we improve two of our previously developed tools that efficiently compute statistics of correlated evolution to characterize the nature, such as synergy or antagonism, and the strength of the interdependence between the traits.Furthermore, we improved the running time and implemented several additional features, such as genetic mapping, Bayesian Markov Chain Monte Carlo estimation, consideration of missing data and phylogenetic uncertainty.As an application, we scan a published penicillin resistance data set ofStreptococcus pneumoniaeand characterize genetic mutations that correlate with antibiotic resistance. The pipeline is accessible both as a self-contained github repository (https://github.com/Maxime5G/EvoScope) and through a graphical galaxy interface (https://galaxy.pasteur.fr/u/maximeg/w/evoscope).
Published: 2022
Full Text: View/download PDF

13. Évolution corrélée : modèles et méthodes

Author: Guillaume ACHAZ and Julien Y. DUTHEIL
Abstract: Les différents caractères portés par les espèces évoluent simultanément au cours du temps. « Caractère » est pris ici au sens large : il peut s'agir de traits quantitatifs, comme la taille ou le poids, ou de traits discrets, comme les nucléotides présents en différents sites d'une macromolécule. Étudier le niveau de dépendance entre l'évolution de plusieurs caractères a motivé le développement d'approches spécifiques selon leurs types.
Published: 2022
Full Text: View/download PDF

14. ViralORFeome: an integrated database to generate a versatile collection of viral ORFs.

Author: J. Pellet, Lionel Tafforeau, M. Lucas-Hourani, Vincent Navratil, Laurène Meyniel, Guillaume Achaz, A. Guironnet-Paquet, A. Aublin-Gex, Grégory Caignard, P. Cassonnet, A. Chaboud, T. Chantier, A. Deloire, C. Demeret, M. Le Breton, Gregory Neveu, L. Jacotot, Vaglio Vaglio, Stéphane Delmotte, Christian Gautier, Christophe Combet, Gilbert Deléage, M. Favre, F. Tangy, Yves Jacob, Patrice André, Vincent Lotteau, Chantal Rabourdin-Combe, and P. O. Vidalain
Published: 2010
Full Text: View/download PDF

15. An appeal for an objective, open, and transparent scientific debate about the origin of SARS-CoV-2

Author: Richard H. Ebright, Etienne Decroly, Milton Leitenberg, Serge Morand, Didier Casane, François Graner, José Halloy, Rossana Segreto, Bruno Canard, Fabien Colombo, Colin D. Butler, Jean-Michel Claverie, Jacques van Helden, Nikolai Petrovsky, Guillaume Achaz, Virginie Courtier, Theories and Approaches of Genomic Complexity (TAGC), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Australian National University (ANU), Muséum national d'Histoire naturelle (MNHN), Architecture et fonction des macromolécules biologiques (AFMB), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Unité de Recherche IRD 072, Laboratoire Evolution, Génomes, Comportement, Ecologie, Centre National de la Recherche Scientifique (CNRS), Aix Marseille Université (AMU), Université Bordeaux Montaigne, Institut Jacques Monod (IJM (UMR_7592)), Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), Rutgers University [Newark], Rutgers University System (Rutgers), Matière et Systèmes Complexes (MSC (UMR_7057)), University of Maryland [College Park], University of Maryland System, Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UR226, Flinders University [Adelaide, Australia], University of Innsbruck, Laboratoire Interdisciplinaire des Energies de Demain (LIED (UMR_8236)), Centre interdisciplinaire de recherche en biologie (CIRB), Labex MemoLife, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Collège de France (CdF (institution))-Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Evolution, génomes, comportement et écologie (EGCE), Institut de Recherche pour le Développement (IRD)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Information génomique et structurale (IGS), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Université Bordeaux Montaigne (UBM), Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Matière et Systèmes Complexes (MSC), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), Leopold Franzens Universität Innsbruck - University of Innsbruck, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE), and Spinelli, Lionel
Subjects: 0303 health sciences, 2019-20 coronavirus outbreak, Coronavirus disease 2019 (COVID-19), SARS-CoV-2, business.industry, [SDV]Life Sciences [q-bio], Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Appeal, COVID-19, General Medicine, Public relations, Biology, 16. Peace & justice, [SDV] Life Sciences [q-bio], 03 medical and health sciences, 0302 clinical medicine, [SDV.SPEE] Life Sciences [q-bio]/Santé publique et épidémiologie, Correspondence, Humans, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, Scientific debate, business, ComputingMilieux_MISCELLANEOUS, 030217 neurology & neurosurgery, 030304 developmental biology
Abstract: International audience
Published: 2021
Full Text: View/download PDF

16. A Novel Heuristic for Local Multiple Alignment of Interspersed DNA Repeats.

Author: Todd J. Treangen, Aaron E. Darling, Guillaume Achaz, Mark A. Ragan, Xavier Messeguer, and Eduardo P. C. Rocha
Published: 2009
Full Text: View/download PDF

17. Interpreting the pervasive observation of U-shaped Site Frequency Spectra

Author: Fabian Freund, Elise Kerdoncuff, Sebastian Matuszewski, Marguerite Lapierre, Marcel Hildebrandt, Jeffrey D. Jensen, Luca Ferretti, Amaury Lambert, Timothy B. Sackton, and Guillaume Achaz
Subjects: Cancer Research, Genetics, Molecular Biology, Genetics (clinical), Ecology, Evolution, Behavior and Systematics
Abstract: The standard neutral model of molecular evolution has traditionally been used as the null model for population genomics. We gathered a collection of 45 genome-wide site frequency spectra from a diverse set of species, most of which display an excess of low and high frequency variants compared to the expectation of the standard neutral model, resulting in U-shaped spectra. We show that multiple merger coalescent models often provide a better fit to these observations than the standard Kingman coalescent. Hence, in many circumstances these under-utilized models may serve as the more appropriate reference for genomic analyses. We further discuss the underlying evolutionary processes that may result in the widespread U-shape of frequency spectra.
Published: 2022
Full Text: View/download PDF

18. mold, a novel software to compile accurate and reliable DNA diagnoses for taxonomic descriptions

Author: Alexander Fedosov, Guillaume Achaz, Andrey Gontchar, Nicolas Puillandre, Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Russian Academy of Sciences [Moscow] (RAS), Éco-Anthropologie (EA), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Centre interdisciplinaire de recherche en biologie (CIRB), Labex MemoLife, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Collège de France (CdF (institution))-Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Dmitry Rogachev Federal Research and Clinical Center of Pediatric Hematology, Oncology and Immunology, Moscow, and European Project: 865101,HYPERDIVERSE
Subjects: Reproducibility of Results, DNA, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, DNA character, Systematics, Genetics, DNA Barcoding, Taxonomic, DNA diagnosis, Sequence Alignment, Ecology, Evolution, Behavior and Systematics, Phylogeny, Software, Biotechnology, Taxonomy
Abstract: International audience; DNA data are increasingly being used for phylogenetic inference, and taxon delimitation and identification, but scarcely for the formal description of taxa, despite their undisputable merits in taxonomy. The uncertainty regarding the robustness of DNA diagnoses, however, remains a major impediment to their use. We have developed a new program, mold, that identifies diagnostic nucleotide combinations (DNCs) in DNA sequence alignments for selected taxa, which can be used to provide formal diagnoses of these taxa. To test the robustness of DNA diagnoses, we carry out iterated haplotype subsampling for selected query species in published DNA data sets of varying complexity. We quantify the reliability of diagnosis by diagnosing each query subsample and then checking if this diagnosis remains valid against the entire data set. We demonstrate that widely used types of diagnostic DNA characters are often absent for a query taxon or are not sufficiently reliable. We thus propose a new type of DNA diagnosis, termed "redundant DNC" (or rDNC), which takes into account unsampled genetic diversity, and constitutes a much more reliable descriptor of a taxon. mold successfully retrieves rDNCs for all but two species in the analysed data sets, even in those comprising hundreds of species. mold shows unparalleled efficiency in large DNA data sets and is the only available software capable of compiling DNA diagnoses that suit predefined criteria of reliability.
Published: 2022
Full Text: View/download PDF

19. Origin and fate of repeats in bacteria.

Author: Guillaume Achaz, Eduardo P. C. Rocha, P. Netter, and Eric Coissac
Published: 2002
Full Text: View/download PDF

20. Repseek, a tool to retrieve approximate repeats from large DNA sequences.

Author: Guillaume Achaz, Frédéric Boyer, Eduardo P. C. Rocha, Alain Viari, and Eric Coissac
Published: 2007
Full Text: View/download PDF

21. Involvement of

Author: Maha, Dahawi, Mohamed S, Elmagzoub, Elhami, A Ahmed, Sara, Baldassari, Guillaume, Achaz, Fatima A, Elmugadam, Wasma A, Abdelgadir, Stéphanie, Baulac, Julien, Buratti, Omer, Abdalla, Sahar, Gamil, Maha, Alzubeir, Rayan, Abubaker, Eric, Noé, Liena, Elsayed, Ammar E, Ahmed, and Eric, Leguern
Subjects: ADGRV1, genetic generalized epilepsy, oligogenism, absence epilepsy, Neurology, susceptibility gene, Original Research
Abstract: Background: Genetic generalized epilepsies (GGE) including childhood absence epilepsy (CAE), juvenile absence epilepsy (JAE), juvenile myoclonic epilepsy (JME), and GGE with tonic–clonic seizures alone (GGE-TCS), are common types of epilepsy mostly determined by a polygenic mode of inheritance. Recent studies showed that susceptibility genes for GGE are numerous, and their variants rare, challenging their identification. In this study, we aimed to assess GGE genetic etiology in a Sudanese population. Methods: We performed whole-exome sequencing (WES) on DNA of 40 patients from 20 Sudanese families with GGE searching for candidate susceptibility variants, which were prioritized by CADD software and functional features of the corresponding gene. We assessed their segregation in 138 individuals and performed genotype–phenotype correlations. Results: In a family including three sibs with GGE-TCS, we identified a rare missense variant in ADGRV1 encoding an adhesion G protein-coupled receptor V1, which was already involved in the autosomal recessive Usher type C syndrome. In addition, five other ADGRV1 rare missense variants were identified in four additional families and absent from 119 Sudanese controls. In one of these families, an ADGRV1 variant was found at a homozygous state, in a female more severely affected than her heterozygous brother, suggesting a gene dosage effect. In the five families, GGE phenotype was statistically associated with ADGRV1 variants (0R = 0.9 103). Conclusion: This study highly supports, for the first time, the involvement of ADGRV1 missense variants in familial GGE and that ADGRV1 is a susceptibility gene for CAE/JAE and GGE-TCS phenotypes.
Published: 2021

22. Simulation of bacterial populations with SLiM

Author: Guillaume Achaz, Flora Jay, Benjamin C. Haller, Jean Cury, Laboratoire de Recherche en Informatique (LRI), CentraleSupélec-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Cornell University [New York], Éco-Anthropologie (EAE), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Centre interdisciplinaire de recherche en biologie (CIRB), Labex MemoLife, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Collège de France (CdF (institution))-Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), TAckling the Underspecified (TAU), Inria Saclay - Ile de France, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire Interdisciplinaire des Sciences du Numérique (LISN), CentraleSupélec-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-CentraleSupélec-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-CentraleSupélec-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), BioInformatique (BioInfo), Laboratoire Interdisciplinaire des Sciences du Numérique (LISN), Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Science des Données (SDD), Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Éco-Anthropologie (EA), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS-PSL), Jay, Flora, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-Collège de France (CdF (institution))-École normale supérieure - Paris (ENS Paris), and Université Paris sciences et lettres (PSL)-Collège de France (CdF (institution))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, Computer science, Population genetics, Genomic data, Distributed computing, [SDV.GEN] Life Sciences [q-bio]/Genetics, computer.software_genre, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, Documentation, Protocol (object-oriented programming), [SDV.MP] Life Sciences [q-bio]/Microbiology and Parasitology, SLiM, [INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM], 030304 developmental biology, Flexibility (engineering), 0303 health sciences, [SDV.GEN]Life Sciences [q-bio]/Genetics, SIMPLE (military communications protocol), Bacteria, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Scripting language, Key (cryptography), Simulator, [INFO.INFO-MO] Computer Science [cs]/Modeling and Simulation, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], computer, Simulation
Abstract: Simulation of genomic data is a key tool in population genetics, yet, to date, there is no forward-in-time simulator of bacterial populations that is both computationally efficient and adaptable to a wide range of scenarios. Here we demonstrate how to simulate bacterial populations with SLiM, a forward-in-time simulator built for eukaryotes. SLiM has gained many users in recent years, due to its speed and power, and has extensive documentation showcasing various scenarios that it can simulate. This paper focuses on a simple demographic scenario, to explore unique aspects of modeling bacteria in SLiM’s scripting language. In addition, we illustrate the flexibility of SLiM by simulating the growth of bacteria on a Petri dish with antibiotic. To foster the development of bacterial simulations based upon this recipe, we explain the inner workings of its code. We also validate the simulator, by extensively testing the results of simulations against existing simulators, and against theoretical expectations for some summary statistics. This protocol, with the flexibility and power of SLiM, will enable the community to simulate bacterial populations efficiently under a wide range of evolutionary scenarios.
Published: 2021
Full Text: View/download PDF

23. The rapid divergence of the Antarctic crinoid species Promachocrinus kerguelensis

Author: Yacine Ben Chehida, Guillaume Achaz, Cyril Gallut, Marc Eléaume, Groningen Institute for Evolutionary Life Sciences [Groningen] (GELIFES), University of Groningen [Groningen], Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), and Fontaine lab
Subjects: 0106 biological sciences, Species complex, Lineage (evolution), Speciation, [SDV]Life Sciences [q-bio], Biodiversity, Allopatric speciation, Biology, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, Genetic drift, Species delimitation, 14. Life underwater, Endemism, Southern Ocean, Promachocrinus kergulensis, 030304 developmental biology, 0303 health sciences, Ecology, Florometra mawsoni, Marine invertebrates, Crinoid, biology.organism_classification, Crinoids, "apparent" drift, Cryptic species, Recent divergence, [SDE]Environmental Sciences
Abstract: Climatic oscillations in Antarctica caused a succession of expansion and reduction of the ice sheets covering the continental shelf of the Southern Ocean. For marine invertebrates, these successions are suspected to have driven allopatric speciation, endemism and the prevalence of cryptic species, leading to the so-called Antarctic ‘biodiversity pump’ hypothesis. Here we took advantage of the recent sampling effort influenced by the International Polar Year (2007-8) to test for the validity of this hypothesis for 1,797 samples of two recognized crinoid species:Promachocrinus kerguelensisandFlorometra mawsoni. Species delimitation analysis identified seven phylogroups. As previously suggested,Promachocrinus kerguelensisforms a complex of six cryptic species. Conversely, despite the morphological differences, our results show thatFlorometra mawsoniis a lineage nested withinPromachocrinus kerguelensis. It suggests thatFlorometra mawsoniandPromachocrinus kerguelensisbelong to the same complex of species. Furthermore, this study indicates that over time and space the different sectors of the Southern Ocean show a remarkable rapid turn-over in term of phylogroups composition and also of genetic variants within phylogroups. We argue that strong “apparent” genetic drift causes this rapid genetic turn-over. Finally, we dated the last common ancestor of all phylogroups at less than 1,000 years, raising doubts on the relevance of the Antarctic “biodiversity pump” for this complex of species. This work is a first step towards a better understanding of how life is diversifying in the Southern Ocean.
Published: 2020

24. The quiescent X, the replicative Y and the Autosomes

Author: Serge Gangloff, Benoit Arcangioli, Guillaume Achaz, Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Centre interdisciplinaire de recherche en biologie (CIRB), Labex MemoLife, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Collège de France (CdF (institution))-Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Dynamique du Génome - Dynamics of the genome, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), This work was supported by the grants ANR-13-BSV8-0018 and ANR-12-BSV7-0012 Demochips from the Agence Nationale de la Recherche (France) to BA and GA, respectively., ANR-13-BSV8-0018,quiescenceDNA,stabilité génétique en quiescence(2013), ANR-12-BSV7-0012,demochips,Inférence de l'histoire démographique à partie des grands jeux de données de polymorphisme A.D.N.(2012), Gangloff, Serge, Blanc 2013 - stabilité génétique en quiescence - - quiescenceDNA2013 - ANR-13-BSV8-0018 - Blanc 2013 - VALID, BLANC - Inférence de l'histoire démographique à partie des grands jeux de données de polymorphisme A.D.N. - - demochips2012 - ANR-12-BSV7-0012 - BLANC - VALID, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS-PSL), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), This work was supported by the grants ANR-13-BSV8-0018 and ANR-12-BSV7-0012 Demochips from the Agence Nationale de la Recherche(France) to BA and GA, respectively., Muséum national d'Histoire naturelle (MNHN)-École Pratique des Hautes Études (EPHE), Génétique des génomes - Genetics of Genomes (UMR 3525), Département de Génomes et Génétique - Department of Genomes and Genetics, and Institut Pasteur [Paris] (IP)-Université Paris Cité (UPCité)
Subjects: Genetics, 0303 health sciences, Mutation, Autosome, Lineage (genetic), [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], [SDV]Life Sciences [q-bio], food and beverages, Biology, medicine.disease_cause, [SDV] Life Sciences [q-bio], 03 medical and health sciences, 0302 clinical medicine, Anisogamy, medicine, Human genome, 1000 Genomes Project, Indel, 030217 neurology & neurosurgery, X chromosome, 030304 developmental biology
Abstract: From the analysis of the mutation spectrum in the 2,504 sequenced human genomes from the 1000 genomes project (phase 3), we show that sexual chromosomes (X and Y) exhibit a different proportion of indel mutations than autosomes (A), ranking them X>A>Y. We further show that X chromosomes exhibit a higher ratio of deletion/insertion when compared to autosomes. This simple pattern shows that the recent report that non-dividing quiescent yeast cells accumulate relatively more indels (and particularly deletions) than replicating ones also applies to metazoan cells, including humans. Indeed, the X chromosomes display more indels than the autosomes, having spent more time in quiescent oocytes, whereas the Y chromosomes are solely present in the replicating spermatocytes. From the proportion of indels, we have inferred that de novo mutations arising in the maternal lineage are twice more likely to be indels than mutations from the paternal lineage. Our observation, consistent with a recent trio analysis of the spectrum of mutations inherited from the maternal lineage, is likely a major component in our understanding of the origin of anisogamy.
Published: 2020
Full Text: View/download PDF

25. The genomic view of diversification

Author: Julie Marin, Amaury Lambert, Guillaume Achaz, Anton Crombach, Centre interdisciplinaire de recherche en biologie (CIRB), Labex MemoLife, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Collège de France (CdF (institution))-Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Éco-Anthropologie (EA), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Artificial Evolution and Computational Biology (BEAGLE), Laboratoire d'InfoRmatique en Image et Systèmes d'information (LIRIS), Université Lumière - Lyon 2 (UL2)-École Centrale de Lyon (ECL), Université de Lyon-Université de Lyon-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Université Lumière - Lyon 2 (UL2)-École Centrale de Lyon (ECL), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Inria Grenoble - Rhône-Alpes, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Probabilités, Statistique et Modélisation (LPSM (UMR_8001)), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS Paris), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Éco-Anthropologie (EAE), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Inria Grenoble - Rhône-Alpes, Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire d'InfoRmatique en Image et Systèmes d'information (LIRIS), Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-École Centrale de Lyon (ECL), Université de Lyon-Université Lumière - Lyon 2 (UL2)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-École Centrale de Lyon (ECL), Université de Lyon-Université Lumière - Lyon 2 (UL2), Laboratoire de Probabilités, Statistiques et Modélisations (LPSM (UMR_8001)), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), and Crombach, Anton
Subjects: 0301 basic medicine, 0106 biological sciences, Genetic Speciation, [SDV]Life Sciences [q-bio], introgression, Population genetics, Inference, Diversification (marketing strategy), Biology, phylogeny, 010603 evolutionary biology, 01 natural sciences, species tree, Gene flow, Coalescent theory, 03 medical and health sciences, Genetic drift, Genetic algorithm, Gene, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, coalescent theory, 0303 health sciences, Genome, Hierarchy (mathematics), Models, Genetic, Gene tree, population genetics, Reproductive isolation, [SDV] Life Sciences [q-bio], Tree (data structure), multispecies coalescent, 030104 developmental biology, gene tree, speciation, Evolutionary biology, gene‐based diversification model, gene flow
Abstract: Evolutionary relationships between species are traditionally represented in the form of a tree, called the species tree. The reconstruction of the species tree from molecular data is hindered by frequent conflicts between gene genealogies. A standard way of dealing with this issue is to pos-tulate the existence of a unique species tree where disagreements between gene trees are explained by incomplete lineage sorting (ILS) due to random coalescences of gene lineages inside the edges of the species tree. This paradigm, known as the multi-species coalescent (MSC), is constantly violated by the ubiquitous presence of gene flow revealed by empirical studies, leading to topological incon-gruences of gene trees that cannot be explained by ILS alone. Here we argue that this paradigm should be revised in favor of a vision acknowledging the importance of gene flow and where gene histories shape the species tree rather than the opposite. We propose a new, plastic framework for modeling the joint evolution of gene and species lineages relaxing the hierarchy between the species tree and gene trees. As an illustration, we implement this framework in a mathematical model called the genomic diversification (GD) model based on coalescent theory, with four parameters tuning repli-cation, genetic differentiation, gene flow and reproductive isolation. We use it to evaluate the amount of gene flow in two empirical data-sets. We find that in these data-sets, gene tree distributions are better explained by the best fitting GD model than by the best fitting MSC model. This work should pave the way for approaches of diversification using the richer signal contained in genomic evolution-ary histories rather than in the mere species tree.
Published: 2020
Full Text: View/download PDF

26. A minimal yet flexible likelihood framework to assess correlated evolution

Author: Abdelkader Behdenna, Maxime Godfroid, Patrice Petot, Joël Pothier, Camille Nous, Amaury Lambert, and Guillaume Achaz
Subjects: Sequence, Mutation rate, Phylogenetic tree, Estimation theory, Computer science, Trait, Range (statistics), Algorithm, Selection (genetic algorithm), Independence (probability theory)
Abstract: An evolutionary process is reflected in the sequence of changes through time of any trait (e.g. morphological, molecular). Yet, a better understanding of evolution would be procured by characterizing correlated evolution, or when two or more evolutionary processes interact. A wide range of parametric methods have previously been proposed to detect correlated evolution but they often require significant computing time as they rely on the estimation of many parameters. Here we propose a minimal likelihood framework modelling the joint evolution of two traits on a known phylogenetic tree. The type and strength of correlated evolution is characterized by few parameters tuning mutation rates of each trait and interdependencies between these rates. The framework can be applied to study any discrete trait or character ranging from nucleotide substitution to gain or loss of a biological function. More specifically, it can be used to 1) test for independence between two evolutionary processes, 2) identify the type of interaction between them and 3) estimate parameter values of the most likely model of interaction. In its current implementation, the method takes as input a phylogenetic tree together with mapped discrete evolutionary events on it and then maximizes the likelihood for one or several chosen scenarios. The strengths and limits of the method, as well as its relative power when compared to a few other methods, are assessed using both simulations and data from 16S rRNA sequences in a sample of 54 γ-enterobacteria. We show that even with datasets of less than 100 species, the method performs well in parameter estimation and in the selection of evolutionary scenario.
Published: 2020
Full Text: View/download PDF

27. Clinical and genetic study of Tunisian families with genetic generalized epilepsy: contribution of CACNA1H and MAST4 genes

Author: Saloua Mrabet, Caroline Nava, Imen Kacem, Eric LeGuern, Mouna Ben Djebara, Riadh Gouider, Eric Noé, A. Gargouri-Berrechid, Guillaume Achaz, Zied Landoulsi, Stéphanie Baulac, and Fatma Laatar
Subjects: Adult, Male, 0301 basic medicine, Proband, Multifactorial Inheritance, Candidate gene, Tunisia, Adolescent, Genetic Linkage, Pedigree chart, Protein Serine-Threonine Kinases, Quantitative trait locus, Cohort Studies, Calcium Channels, T-Type, Consanguinity, Young Adult, 03 medical and health sciences, Cellular and Molecular Neuroscience, 0302 clinical medicine, Childhood absence epilepsy, Genetics, CACNA1H, medicine, Humans, Family, Genetic Predisposition to Disease, Age of Onset, Child, Genetic Association Studies, Genetics (clinical), biology, Oligogenic Inheritance, medicine.disease, Pedigree, 030104 developmental biology, biology.protein, Epilepsy, Generalized, Female, Juvenile myoclonic epilepsy, Microtubule-Associated Proteins, 030217 neurology & neurosurgery
Abstract: Genetic generalized epilepsies (GGE) (childhood absence epilepsy (CAE), juvenile myoclonic epilepsy (JME) and epilepsy with generalized tonic-clonic seizures (GTCS)) are mainly determined by genetic factors. Since few mutations were identified in rare families with autosomal dominant GGE, a polygenic inheritance was suspected in most patients. Recent studies on large American or European cohorts of sporadic cases showed that susceptibility genes were numerous although their variants were rare, making their identification difficult. Here, we reported clinical and genetic characteristics of 30 Tunisian GGE families, including 71 GGE patients. The phenotype was close to that in sporadic cases. Nineteen pedigrees had a homogeneous type of GGE (JME-CAE-CGTS), and 11 combined these epileptic syndromes. Rare non-synonymous variants were selected in probands using a targeted panel of 30 candidate genes and their segregation was determined in families. Molecular studies incriminated different genes, mainly CACNA1H and MAST4. The segregation of at least two variants in different genes in some pedigrees was compatible with the hypothesis of an oligogenic inheritance, which was in accordance with the relatively low frequency of consanguineous probands. Since at least 2 susceptibility genes were likely shared by different populations, genetic factors involved in the majority of Tunisian GGE families remain to be discovered. Their identification should be easier in families with a homogeneous type of GGE, in which an intra-familial genetic homogeneity could be suspected.
Published: 2018
Full Text: View/download PDF

28. No HIV-1 molecular evolution on long-term antiretroviral therapy initiated during primary HIV-1 infection

Author: Aude Jary, Lambert Assoumou, Vincent Calvez, Cathia Soulié, Nathalie Désiré, Guillaume Achaz, Romain Palich, Roland Tubiana, Anne Simon, Christine Katlama, Sophie Brouillet, Thuy Van Nguyen, Basma Abdi, Marc-Antoine Valantin, Sophie Sayon, Anne-Geneviève Marcelin, Marc Wirden, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU), Service de Virologie [CHU Pitié-Salpêtrière], CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Service de Maladies Infectieuses et Tropicales [CHU Pitié-Salpêtrière], Service de médecine interne [CHU Pitié-Salpétrière], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Sorbonne Université (SU), Gestionnaire, Hal Sorbonne Université, Sorbonne Université (SU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Service de virologie [CHU Pitié-Salpêtrière], and Service des maladies infectieuses et tropicales [CHU Pitié-Salpêtrière]
Subjects: 0301 basic medicine, Anti-HIV Agents, [SDV]Life Sciences [q-bio], Immunology, Population, HIV Infections, medicine.disease_cause, Evolution, Molecular, 03 medical and health sciences, 0302 clinical medicine, Molecular evolution, medicine, Humans, Immunology and Allergy, 030212 general & internal medicine, education, Sida, Phylogeny, Retrospective Studies, Mutation, education.field_of_study, Phylogenetic tree, biology, business.industry, Viral Load, biology.organism_classification, Antiretroviral therapy, Virology, 3. Good health, [SDV] Life Sciences [q-bio], 030104 developmental biology, Infectious Diseases, Viral evolution, HIV-1, business, Viral load
Abstract: International audience; Objective: Most studies about HIV-1 molecular evolution have shown the lack of viral evolution on effective antiretroviral therapy (ART), although controversial results have been documented. We therefore aimed to look for evidence of HIV-1 evolution in patients who initiated ART at the time of primary HIV-1 infection (PHI).Design: We included retrospectively 20 patients diagnosed at PHI, treated at the time of acute infection and with subsequent effective long-term suppressive ART (HIV viral load
Published: 2020
Full Text: View/download PDF

29. Revisiting use of DNA characters in taxonomy with MolD - a tree independent algorithm to retrieve diagnostic nucleotide characters from monolocus datasets

Author: Alexander E. Fedosov, Guillaume Achaz, and Nicolas Puillandre
Subjects: chemistry.chemical_classification, Systematics, Species complex, Computer science, Robustness (evolution), DNA sequencing, chemistry.chemical_compound, Taxon, chemistry, Nucleotide, A-DNA, Taxonomy (biology), Algorithm, DNA
Abstract: While DNA characters are increasingly used for phylogenetic inference, taxa delimitation and identification, their use for formal description of taxa (i.e. providing either a formal description or a diagnosis) remains scarce and inconsistent. The impediments are neither nomenclatural, nor conceptual, but rather methodological issues: lack of agreement of what DNA character should be provided, and lack of a suitable operational algorithm to identify such characters. Furthermore, the reluctance of using DNA data in taxonomy may also be due to the concerns of insufficient reliability of DNA characters as robustness of the DNA based diagnoses has never been thoroughly assessed. Removing these impediments will enhance integrity of systematics, and will enable efficient treatment of traditionally problematic cases, such as for example, cryptic species. We have developed a novel versatile and scalable algorithm MolD to recover diagnostic combinations of nucleotides (DNCs) for pre-defined groups of DNA sequences, corresponding to taxa. We applied MolD to four published monolocus datasets to examine 1) which type of DNA characters compilation allows for more robust diagnosis, and 2) how the robustness of DNA based diagnosis changes depending on the sampled fraction of taxons diversity. We demonstrate that the redundant DNCs, termed herein sDNCs, allow for higher robustness. Furthermore, we show that a reliable DNA-based diagnosis may be obtained when a rather small fraction of the entire data set is available. Based on our results we propose improvements to the existing practices of handling DNA data in taxonomic descriptions, and discuss a workflow of contemporary systematic study, where the integrative taxonomy part precedes the proposition of a DNA based diagnosis and the diagnosis itself can be efficiently used as a DNA barcode. Our analysis fills existing methodological gaps, thus setting stage for a wider use of the DNA data in taxa description.
Published: 2019
Full Text: View/download PDF

30. ASAP: assemble species by automatic partitioning

Author: Nicolas Puillandre, Guillaume Achaz, Sophie Brouillet, Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA)
Subjects: 0106 biological sciences, 0301 basic medicine, Scoring system, Biology, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, Barcode, computer.software_genre, 010603 evolutionary biology, 01 natural sciences, DNA barcoding, law.invention, Coalescent theory, 03 medical and health sciences, Species Specificity, law, Genetics, Cluster Analysis, DNA Barcoding, Taxonomic, ComputingMilieux_MISCELLANEOUS, Ecology, Evolution, Behavior and Systematics, Phylogeny, Single locus, Phylogenetic reconstruction, Hierarchical clustering, 030104 developmental biology, Pairwise comparison, Data mining, computer, Monte Carlo Method, Sequence Alignment, Algorithms, Software, Biotechnology
Abstract: Here, we describe Assemble Species by Automatic Partitioning (ASAP), a new method to build species partitions from single locus sequence alignments (i.e., barcode data sets). ASAP is efficient enough to split data sets as large 104 sequences into putative species in several minutes. Although grounded in evolutionary theory, ASAP is the implementation of a hierarchical clustering algorithm that only uses pairwise genetic distances, avoiding the computational burden of phylogenetic reconstruction. Importantly, ASAP proposes species partitions ranked by a new scoring system that uses no biological prior insight of intraspecific diversity. ASAP is a stand-alone program that can be used either through a graphical web-interface or that can be downloaded and compiled for local usage. We have assessed its power along with three others programs (ABGD, PTP and GMYC) on 10 real COI barcode data sets representing various degrees of challenge (from small and easy cases to large and complicated data sets). We also used Monte-Carlo simulations of a multispecies coalescent framework to assess the strengths and weaknesses of ASAP and the other programs. Through these analyses, we demonstrate that ASAP has the potential to become a major tool for taxonomists as it proposes rapidly in a full graphical exploratory interface relevant species hypothesis as a first step of the integrative taxonomy process.
Published: 2019
Full Text: View/download PDF

31. Correction: The landscape of epilepsy-related GATOR1 variants

Author: Johannes R. Lemke, Thomas Dorn, Laura Hernandez-Hernandez, Giuseppe d'Orsi, Eveline Hagebeuk, Annapurna Poduri, Douglas R. NordliJr, Hélène Catenoix, Melanie Jennesson, Veronique Darmency, Kevin Rostasy, Thomas Becher, Laura Licchetta, Peter Uldall, Lysa Boissé Lomax, Bianca Berghuis, Ilona Krey, Gaetan Lesca, Anne de Saint Martin, Boudewijn Gunning, Anne Fabienne Lepine, Renske Oegema, Brigitte Ricard-Mousnier, Sarah Ferrand-Sorbets, Arnaud Biraben, Charles Deckers, An Sofie Schoonjans, Martin Zenker, Simona Balestrini, Inga Talvik, Julitta de Bellescize, Christopher J. Yuskaitis, Georg Dorfmüller, Erik H. Niks, Guillaume Achaz, Laurence Faivre, Pasquale Striano, Shifteh Sattar, Karen Müller-Schlüter, Sanjay M. Sisodiya, Caroline Nava, Pia Zacher, Fabrice Bartolomei, Kristin Lindstrom, Sophie Julia, Eric LeGuern, Thomas Cloppenborg, Rikke S. Møller, Antonio Gambardella, Mathilde Chipaux, Sara Baldassari, Pavel Krsek, Marie Line Jacquemont, Ilse Wegner, Christian Brandt, Barbora Benova, Valerio Conti, Gabrielle Rudolf, Floor E. Jansen, Edouard Hirsch, S. Krithika, Jamel Chelly, Katrien Stouffs, Daniëlle de Jong, Courtney Kiss, Tilman Polster, Eva H. Brilstra, Tommaso Pippucci, Markus Wolff, Cécile Marchal, Giovanni Crichiutti, Kees P.J. Braun, Paolo Tinuper, Stéphanie Baulac, Valentin Sander, Anne-Sophie Lebre, Nienke E. Verbeek, Anna Jansen, Francesca Bisulli, Fabienne Picard, Natasha E. Schoeler, Julien Thevenon, Marjan J. A. van Kempen, Guido Rubboli, Sarah Weckhuysen, Renzo Guerrini, Eleni Panagiotakaki, Meral Balci, Institut du Cerveau et de la Moëlle Epinière = Brain and Spine Institute (ICM), Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Hôpital Universitaire de Genève, Department of Genetics [Utrecht, the Netherlands], University Medical Center [Utrecht], Children's Hospital A. Meyer, Department of Clinical and Experimental Epilepsy, University College of London [London] (UCL), Molecular Cell Biology, Leiden University Medical Center (LUMC), Danish Epilepsy Centre, Denmark and Aarhus University, Aarhus, Centre Hospitalier Universitaire de La Réunion (CHU La Réunion), Service de Génétique Cytogénétique et Embryologie [CHU Pitié-Salpêtrière], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Neurogénétique Moléculaire et Cellulaire, Institut Naltional de la Santé et de la Recherche Médicale, Epidémiologie et analyses en santé publique : risques, maladies chroniques et handicaps (LEASP), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM), Regional Epilepsy Center, Reggio Calabria, Centre de génétique - Centre de référence des maladies rares, anomalies du développement et syndromes malformatifs (CHU de Dijon), Centre Hospitalier Universitaire de Dijon - Hôpital François Mitterrand (CHU Dijon), FHU TRANSLAD (CHU de Dijon), Département de Sociologie [université de Bourgogne], UFR de sciences humaines [Université de Bourgogne], Université de Bourgogne (UB)-Université de Bourgogne (UB), Service de Neurophysiologie Clinique (CHU Dijon), Laboratoire Traitement du Signal et de l'Image (LTSI), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Santé et de la Recherche Médicale (INSERM), Service de génétique [Reims], Centre Hospitalier Universitaire de Reims (CHU Reims), Universitair Ziekenhuis Brussel, Equipe GAD (LNC - U1231), Lipides - Nutrition - Cancer [Dijon - U1231] (LNC), Université de Bourgogne (UB)-Institut National de la Santé et de la Recherche Médicale (INSERM)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université de Bourgogne (UB)-Institut National de la Santé et de la Recherche Médicale (INSERM)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Université Bourgogne Franche-Comté [COMUE] (UBFC), Département d'Epilepsie, Sommeil et Neurophysiologie Pédiatrique [HCL, Lyon], Hospices Civils de Lyon (HCL), Institute of Human Genetics, University Hospital Magdeburg, Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), University of Southern Denmark (SDU), Institut du Cerveau = Paris Brain Institute (ICM), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Sorbonne Université (SU)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Hôpital Universitaire de Genève = University Hospitals of Geneva (HUG), Universiteit Leiden-Universiteit Leiden, Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM), Université de Rennes (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM), Muséum national d'Histoire naturelle (MNHN)-École Pratique des Hautes Études (EPHE), Centre interdisciplinaire de recherche en biologie (CIRB), Labex MemoLife, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Collège de France (CdF (institution))-Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), and Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)
Subjects: 0303 health sciences, business.industry, Published Erratum, MEDLINE, medicine.disease, computer.software_genre, Spelling, 03 medical and health sciences, Epilepsy, 0302 clinical medicine, [SDV.GEN.GH]Life Sciences [q-bio]/Genetics/Human genetics, medicine, Artificial intelligence, business, Psychology, computer, 030217 neurology & neurosurgery, Genetics (clinical), Natural language processing, 030304 developmental biology
Abstract: International audience; The original version of this article contained an error in the spelling of the author Erik H. Niks, which was incorrectly given as Erik Niks. This has now been corrected in both the PDF and HTML versions of the article.
Published: 2019
Full Text: View/download PDF

32. Is reproductive strategy a key factor in understanding the evolutionary history of Southern Ocean Asteroidea (Echinodermata)?

Author: Quentin Jossart, Marc Eleaume, Bruno Danis, Thomas Saucède, Chester J. Sands, Guillaume Achaz, Camille Moreau, Antonio Agüera, Laboratoire de Biologie Marine, Université libre de Bruxelles (ULB), Biogéosciences [UMR 6282] (BGS), Université de Bourgogne (UB)-Centre National de la Recherche Scientifique (CNRS), Marine Biology, Vrije Universiteit Brussel (VUB), Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), British Antarctic Survey (BAS), Natural Environment Research Council (NERC), Centre interdisciplinaire de recherche en biologie (CIRB), Labex MemoLife, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Collège de France (CdF (institution))-Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Fonds pour la formation à la Recherche dans l'Industrie et l'Agriculture' (FRIA)., Laffont, Rémi, Biogéosciences [UMR 6282] [Dijon] (BGS), Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique (CNRS), École normale supérieure - Paris (ENS Paris), and Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS Paris)
Subjects: 0106 biological sciences, trans‐Antarctic seaway, invertebrate, Biology, 010603 evolutionary biology, 01 natural sciences, Santé publique, Environnement et pollution, 03 medical and health sciences, Asteroidea, lcsh:QH540-549.5, emergence, bipolarity, 14. Life underwater, Molecular clock, Ecology, Evolution, Behavior and Systematics, Original Research, 030304 developmental biology, Nature and Landscape Conservation, 0303 health sciences, Genetic diversity, trans-Antarctic seaway, Ecology, Phylogenetic tree, Ecologie, Cytochrome c oxidase subunit I, brooding, thermohaline expressway, [SDE.BE] Environmental Sciences/Biodiversity and Ecology, Colonisation, Phylogeography, Genetic structure, Antarctica, lcsh:Ecology, Species richness, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Echinodermata
Abstract: Life traits such as reproductive strategy can be determining factors of species evolutionary history and explain the resulting diversity patterns. This can be investigated using phylogeographic analyses of genetic units. In this work, the genetic structure of five asteroid genera with contrasting reproductive strategies (brooding: Diplasterias, Notasterias and Lysasterias versus broadcasting: Psilaster and Bathybiaster) was investigated in the Southern Ocean. Over 1,400 mtDNA cytochrome C oxidase subunit I (COI) sequences were analysed using five species delineation methods (ABGD, ASAP, mPTP, sGMYC and mGMYC), two phylogenetic reconstructions (ML and BA), and molecular clock calibrations, in order to examine the weight of reproductive strategy in the observed differences among phylogeographic patterns. We hypothesised that brooding species would show higher levels of genetic diversity and species richness along with a clearer geographic structuring than broadcasting species. In contrast, genetic diversity and species richness were not found to be significantly different between brooders and broadcasters, but broadcasters are less spatially structured than brooders supporting our initial hypothesis and suggesting more complex evolutionary histories associated to this reproductive strategy. Broadcasters' phylogeography can be explained by different scenarios including deep-sea colonisation routes, bipolarity or cosmopolitanism, and sub-Antarctic emergence for the genus Bathybiaster; Antarctic- New Zealand faunal exchanges across the Polar Front for the genus Psilaster. Brooders' phylogeography could support the previously formulated hypothesis of a past trans-Antarctic seaway established between the Ross and the Weddell seas during the Plio-Pleistocene. Our results also show, for the first time, that the Weddell Sea is populated by a mixed asteroid fauna originating from both the East and West Antarctic., SCOPUS: ar.j, info:eu-repo/semantics/published
Published: 2019
Full Text: View/download PDF

33. Testing for population decline using maximal linkage disequilibrium blocks

Author: Elise Kerdoncuff, Amaury Lambert, Guillaume Achaz, Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Centre interdisciplinaire de recherche en biologie (CIRB), Labex MemoLife, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Collège de France (CdF (institution))-Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS-PSL), and CCSD, Accord Elsevier
Subjects: 0301 basic medicine, 0106 biological sciences, Linkage disequilibrium, Range (biology), [SDV]Life Sciences [q-bio], Single-nucleotide polymorphism, Biology, 010603 evolutionary biology, 01 natural sciences, Polymorphism, Single Nucleotide, Linkage Disequilibrium, Coalescent theory, Population genomics, 03 medical and health sciences, Block (programming), Animals, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Population Density, 0303 health sciences, Population size, [SDV] Life Sciences [q-bio], Population decline, 030104 developmental biology, Evolutionary biology, Conservation status, Conservation biology
Abstract: Only 6% of known species have a conservation status. Methods that assess conservation statuses are often based on individual counts and are thus too laborious to be generalized to all species. Population genomics methods that infer past variations in population size are easy to use but limited to the relatively distant past. Here we propose a population genomics approach that tests for recent population decline and may be used to assess species conservation statuses. More specifically, we study Maximal Recombination Free (MRF) blocks, that are segments of a sequence alignment inherited from a common ancestor without recombination. MRF blocks are relatively longer in small than in large populations. We use the distribution of MRF block lengths rescaled by their mean to test for recent population decline. However, because MRF blocks are difficult to detect, we also consider Maximal Linkage Disequilibrium (MLD) blocks, which are runs of single nucleotide polymorphisms compatible with a single tree. We develop a new method capable of inferring a very recent decline (e.g. with a detection power of 50% for populations which size was halved toN, 0.05 ×Ngenerations ago) from rescaled MLD block lengths. Our framework could serve as a basis for quantitative tools to assess conservation status in a wide range of species.
Published: 2019
Full Text: View/download PDF

34. Molecular evolution through the joint lens of genomic and population processes

Author: Guillaume Achaz
Subjects: education.field_of_study, Computer science, Evolutionary biology, Molecular evolution, Population, Lens (geology), General Medicine, education, Joint (geology), Selection (genetic algorithm)
Abstract: A recommendation of: Fanny Pouyet and Kimberly J. Gilbert Towards an improved understanding of molecular evolution: the relative roles of selection, drift, and everything in between http://arxiv.org/abs/1909.11490
Published: 2020
Full Text: View/download PDF

35. Is convergence an evidence for positive selection?

Author: Guillaume Achaz, Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Centre interdisciplinaire de recherche en biologie (CIRB), Labex MemoLife, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Collège de France (CdF (institution))-Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS-PSL), and guillemaud, thomas
Subjects: 0106 biological sciences, 0303 health sciences, Positive selection, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], General Medicine, 010603 evolutionary biology, 01 natural sciences, 3. Good health, 03 medical and health sciences, Convergent evolution, [SDV.BID.EVO] Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Convergence (relationship), Mathematical economics, Selection (genetic algorithm), 030304 developmental biology, Mathematics
Abstract: International audience; A recommendation of the preprint: Frederic Bertels, Karin J Metzner, Roland R Regoes. Convergent evolution as an indicator for selection during acute HIV-1 infection (2018), bioRxiv, 168260, ver. 4 peer-reviewed and recommended by Peer Community in Evolutionary Biology. https://doi.org/10.1101/168260
Published: 2018
Full Text: View/download PDF

36. A Molecular Portrait of De Novo Genes in Yeasts

Author: Joshua J. Coon, Nikolaos Vakirlis, Dana A. Opulente, Chris Todd Hittinger, Gilles Fischer, Alexander S. Hebert, Guillaume Achaz, Ingrid Lafontaine, Biology of Genomes [LCQB] (LCQB-BiG), Biologie Computationnelle et Quantitative = Laboratory of Computational and Quantitative Biology (LCQB), Institut de Biologie Paris Seine (IBPS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Paris Seine (IBPS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Systématique, adaptation, évolution (SAE), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Department of Chemistry, and University of Wisconsin-Madison
Subjects: 0301 basic medicine, Computational biology, Biology, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, Conserved sequence, Evolution, Molecular, Fungal Proteins, 03 medical and health sciences, Saccharomyces, 0302 clinical medicine, Intergenic region, Phylogenetics, Genetics, Selection, Genetic, Promoter Regions, Genetic, Molecular Biology, Gene, Ecology, Evolution, Behavior and Systematics, Discoveries, Conserved Sequence, ComputingMilieux_MISCELLANEOUS, Recombination, Genetic, Fungal protein, Base Sequence, Age Factors, Promoter, Phenotype, 030104 developmental biology, Homologous recombination, 030217 neurology & neurosurgery
Abstract: New genes, with novel protein functions, can evolve "from scratch" out of intergenic sequences. These de novo genes can integrate the cell's genetic network and drive important phenotypic innovations. Therefore, identifying de novo genes and understanding how the transition from noncoding to coding occurs are key problems in evolutionary biology. However, identifying de novo genes is a difficult task, hampered by the presence of remote homologs, fast evolving sequences and erroneously annotated protein coding genes. To overcome these limitations, we developed a procedure that handles the usual pitfalls in de novo gene identification and predicted the emergence of 703 de novo gene candidates in 15 yeast species from 2 genera whose phylogeny spans at least 100 million years of evolution. We validated 85 candidates by proteomic data, providing new translation evidence for 25 of them through mass spectrometry experiments. We also unambiguously identified the mutations that enabled the transition from noncoding to coding for 30 Saccharomyces de novo genes. We established that de novo gene origination is a widespread phenomenon in yeasts, only a few being ultimately maintained by selection. We also found that de novo genes preferentially emerge next to divergent promoters in GC-rich intergenic regions where the probability of finding a fortuitous and transcribed ORF is the highest. Finally, we found a more than 3-fold enrichment of de novo genes at recombination hot spots, which are GC-rich and nucleosome-free regions, suggesting that meiotic recombination contributes to de novo gene emergence in yeasts.
Published: 2018
Full Text: View/download PDF

37. Comparative Genomics of Tenacibaculum dicentrarchi and 'Tenacibaculum finnmarkense' Highlights Intricate Evolution of Fish-Pathogenic Species

Author: Ruben Avendaño-Herrera, Guillaume Achaz, Jean François Bernardet, Sébastien Bridel, Anne Berit Olsen, Hanne Nilsen, Eric Duchaud, Unité de recherche Virologie et Immunologie Moléculaires (VIM), Institut National de la Recherche Agronomique (INRA), FINALAB, Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), Norwegian Veterinary Institute, Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-Université Pierre et Marie Curie - Paris 6 (UPMC)-École pratique des hautes études (EPHE)-Centre National de la Recherche Scientifique (CNRS), Universidad Andrés Bello - UNAB (CHILE), Universidad de Concepción [Chile], Muséum national d'Histoire naturelle (MNHN)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-École pratique des hautes études (EPHE), Unité de recherche Virologie et Immunologie Moléculaires (VIM (UR 0892)), Norwegian Veterinary Institute [Oslo], Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Universidad Andrés Bello [Santiago] (UNAB), EU EMIDA ERA-NET project 'Control Flavobacteriaceae Infections in European Fish farms', Agence Nationale pour la Recherche [ANR-14-CE19-0020], National Infrastructure 'France Genomique' funded as part of the Investissement d'avenir program managed by Agence Nationale pour la Recherche [ANR-10-INBS-09], Comision Nacional de Investigacion Cientifica y Tecnologica (CONICYT, Chile) [FONDECYT 1150695, CONICYT/FONDAP/15110027], and Duchaud, Eric
Subjects: 0301 basic medicine, Tenacibaculum, tenacibaculosis, genomes, fish pathogens, virulence, evolution, Genome evolution, Evolution, Fish farming, [SDV]Life Sciences [q-bio], Zoology, Genomics, Biology, Genome, Fish Diseases, 03 medical and health sciences, Flavobacteriaceae Infections, Phylogenetics, Genetics, Animals, 14. Life underwater, Genomes, Sea bass, Fish pathogens, Phylogeny, Ecology, Evolution, Behavior and Systematics, Comparative genomics, Tenacibaculosis, Virulence, Fishes, Genome Report, 030104 developmental biology, Genome, Bacterial
Abstract: Data deposition: All genome sequencing data have been deposited at the European Nucleotide Archive under the accessions GCA_900239455, GCA_900239305, GCA_900239485, GCA_900239185, GCA_900239505, GCA_900239345, and GCA_900239495.; International audience; The genus Tenacibaculum encompasses several species pathogenic for marine fish. Tenacibaculum dicentrarchi and " Tenacibaculum finnmarkense " (Quotation marks denote species that have not been validly named.) were retrieved from skin lesions of farmed fish such as European sea bass or Atlantic salmon. They cause a condition referred to as tenacibaculosis and severe outbreaks and important fish losses have been reported in Spanish, Norwegian, and Chilean marine farms. We report here the draft genomes of the T. dicentrarchi and " T. finnmarkense " type strains. These genomes were compared with draft genomes from field isolates retrieved from Chile and Norway and with previously published Tenacibaculum genomes. We used Average Nucleotide Identity and core genome-based phylogeny as a proxy index for species boundary delineation. This work highlights evolution of closely related fish-pathogenic species and suggests that homologous recombination likely contributes to genome evolution.
Published: 2018
Full Text: View/download PDF

38. Evolutionary constraints in fitness landscapes

Author: Guillaume Achaz, Daniel M. Weinreich, Luca Ferretti, and Fumio Tajima
Subjects: 0106 biological sciences, 0301 basic medicine, Theoretical computer science, Fitness landscape, Small number, Genetic Fitness, Epistasis, Genetic, Biology, 010603 evolutionary biology, 01 natural sciences, Article, Constraint (information theory), Evolution, Molecular, 03 medical and health sciences, 030104 developmental biology, Similarity (psychology), Genetics, Epistasis, Predictability, Selection, Genetic, Genetics (clinical), Selection (genetic algorithm)
Abstract: In the last years, several genotypic fitness landscapes-combinations of a small number of mutations-have been experimentally resolved. To learn about the general properties of "real" fitness landscapes, it is key to characterize these experimental landscapes via simple measures of their structure, related to evolutionary features. Some of the most relevant measures are based on the selectively acessible paths and their properties. In this paper, we present some measures of evolutionary constraints based on (i) the similarity between accessible paths and (ii) the abundance and characteristics of "chains" of obligatory mutations, that are paths going through genotypes with a single fitter neighbor. These measures have a clear evolutionary interpretation. Furthermore, we show that chains are only weakly correlated to classical measures of epistasis. In fact, some of these measures of constraint are non-monotonic in the amount of epistatic interactions, but have instead a maximum for intermediate values. Finally, we show how these measures shed light on evolutionary constraints and predictability in experimentally resolved landscapes.
Published: 2018

39. The sequential loss of allelic diversity

Author: Guillaume Achaz, Amaury Lambert, and Emmanuel Schertzer
Subjects: Statistics and Probability, Population, Type (model theory), 01 natural sciences, Coalescent theory, Combinatorics, 010104 statistics & probability, Identity (mathematics), FOS: Mathematics, Quantitative Biology::Populations and Evolution, 0101 mathematics, education, Quantitative Biology - Populations and Evolution, Mathematics, education.field_of_study, Extinction, Counting process, 60-06, 60G09, 60J20, 60J70, 92D10, Applied Mathematics, Probability (math.PR), 010102 general mathematics, Populations and Evolution (q-bio.PE), FOS: Biological sciences, Path (graph theory), Constant (mathematics), Mathematics - Probability
Abstract: This paper gives a new flavor of what Peter Jagers and his co-authors call `the path to extinction'. In a neutral population with constant size $N$, we assume that each individual at time $0$ carries a distinct type, or allele. We consider the joint dynamics of these $N$ alleles, for example the dynamics of their respective frequencies and more plainly the nonincreasing process counting the number of alleles remaining by time $t$. We call this process the extinction process. We show that in the Moran model, the extinction process is distributed as the process counting (in backward time) the number of common ancestors to the whole population, also known as the block counting process of the $N$-Kingman coalescent. Stimulated by this result, we investigate: (1) whether it extends to an identity between the frequencies of blocks in the Kingman coalescent and the frequencies of alleles in the extinction process, both evaluated at jump times; (2) whether it extends to the general case of $\Lambda$-Fleming-Viot processes., Comment: Submitted to appear in the Festschrift in honor of Peter Jagers
Published: 2018

40. The landscape of epilepsy-related GATOR1 variants

Author: Johannes R. Lemke, Pia Zacher, Thomas Dorn, Laura Hernandez-Hernandez, Natasha E. Schoeler, Stéphanie Baulac, Sara Baldassari, Anne de Saint Martin, Eleni Panagiotakaki, Anne Fabienne Lepine, Markus Wolff, Arnaud Biraben, Renske Oegema, Edouard Hirsch, Anna Jansen, Charles Deckers, Nienke E. Verbeek, Fabienne Picard, Georg Dorfmüller, Sarah Ferrand-Sorbets, Barbora Benova, Francesca Bisulli, Inga Talvik, Kristin Lindstrom, Tilman Polster, Douglas R. Nordli, Tommaso Pippucci, Eva H. Brilstra, Shifteh Sattar, Erik H. Niks, Marie Line Jacquemont, Kees P.J. Braun, Karen Müller-Schlüter, Sanjay M. Sisodiya, Sarah Weckhuysen, Lysa Boissé Lomax, Sophie Julia, Brigitte Ricard-Mousnier, Mathilde Chipaux, Laura Licchetta, Gaetan Lesca, Bianca Berghuis, S. Krithika, Jamel Chelly, Renzo Guerrini, Hélène Catenoix, Annapurna Poduri, Melanie Jennesson, Pasquale Striano, Rikke S. Møller, Antonio Gambardella, Guillaume Achaz, Peter Uldall, Fabrice Bartolomei, Giuseppe d'Orsi, Laurence Faivre, Floor E. Jansen, An Sofie Schoonjans, Kevin Rostasy, Thomas Becher, Pavel Krsek, Julien Thevenon, Marjan J. A. van Kempen, Guido Rubboli, Cécile Marchal, Meral Balci, Boudewijn Gunning, Ilona Krey, Julitta de Bellescize, Veronique Darmency, Christopher J. Yuskaitis, Daniëlle de Jong, Giovanni Crichiutti, Paolo Tinuper, Katrien Stouffs, Valentin Sander, Anne-Sophie Lebre, Thomas Cloppenborg, Valerio Conti, Gabrielle Rudolf, Courtney Kiss, Eveline Hagebeuk, Caroline Nava, Eric LeGuern, Ilse Wegner, Christian Brandt, Martin Zenker, Simona Balestrini, Picard, Fabienne, Baldassari S., Picard F., Verbeek N.E., van Kempen M., Brilstra E.H., Lesca G., Conti V., Guerrini R., Bisulli F., Licchetta L., Pippucci T., Tinuper P., Hirsch E., de Saint Martin A., Chelly J., Rudolf G., Chipaux M., Ferrand-Sorbets S., Dorfmuller G., Sisodiya S., Balestrini S., Schoeler N., Hernandez-Hernandez L., Krithika S., Oegema R., Hagebeuk E., Gunning B., Deckers C., Berghuis B., Wegner I., Niks E., Jansen F.E., Braun K., de Jong D., Rubboli G., Talvik I., Sander V., Uldall P., Jacquemont M.-L., Nava C., Leguern E., Julia S., Gambardella A., d'Orsi G., Crichiutti G., Faivre L., Darmency V., Benova B., Krsek P., Biraben A., Lebre A.-S., Jennesson M., Sattar S., Marchal C., Nordli D.R., Lindstrom K., Striano P., Lomax L.B., Kiss C., Bartolomei F., Lepine A.F., Schoonjans A.-S., Stouffs K., Jansen A., Panagiotakaki E., Ricard-Mousnier B., Thevenon J., de Bellescize J., Catenoix H., Dorn T., Zenker M., Muller-Schluter K., Brandt C., Krey I., Polster T., Wolff M., Balci M., Rostasy K., Achaz G., Zacher P., Becher T., Cloppenborg T., Yuskaitis C.J., Weckhuysen S., Poduri A., Lemke J.R., Moller R.S., Baulac S., Institut du Cerveau et de la Moëlle Epinière = Brain and Spine Institute (ICM), Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Department of Genetics [Utrecht, the Netherlands], University Medical Center [Utrecht], Service de Génétique [HCL Groupement Hospitalier Est], Groupement Hospitalier Lyon-Est (GHE), Hospices Civils de Lyon (HCL)-Hospices Civils de Lyon (HCL), Centre de recherche en neurosciences de Lyon - Lyon Neuroscience Research Center (CRNL), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet [Saint-Étienne] (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Children's Hospital A. Meyer, Service de Neurologie [Strasbourg], CHU Strasbourg-Hopital Civil, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Department of Clinical and Experimental Epilepsy, University College of London [London] (UCL), Academic Center for Epileptology Kempenhaeghe & Maastricht UMC+ [Heeze], Danish Epilepsy Centre, Denmark and Aarhus University, Aarhus, Centre Hospitalier Universitaire de La Réunion (CHU La Réunion), Service de Génétique Cytogénétique et Embryologie [CHU Pitié-Salpêtrière], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Service de génétique médicale [Toulouse], CHU Toulouse [Toulouse], Centre de génétique - Centre de référence des maladies rares, anomalies du développement et syndromes malformatifs (CHU de Dijon), Centre Hospitalier Universitaire de Dijon - Hôpital François Mitterrand (CHU Dijon), FHU TRANSLAD (CHU de Dijon), Université de Bourgogne (UB), Service de Neurophysiologie Clinique (CHU Dijon), CHU Pontchaillou [Rennes], Service de pédiatrie spécialisée et médecine infantile (neurologie, pneumologie, maladies héréditaires du métabolisme) [Hôpital de la Timone - APHM], Hôpital de la Timone [CHU - APHM] (TIMONE), Epilepsie, sommeil et explorations fonctionnelles neuropédiatriques, Hospices Civils de Lyon (HCL)-Hôpital Femme Mère Enfant, Equipe GAD (LNC - U1231), Lipides - Nutrition - Cancer [Dijon - U1231] (LNC), Université de Bourgogne (UB)-Institut National de la Santé et de la Recherche Médicale (INSERM)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université de Bourgogne (UB)-Institut National de la Santé et de la Recherche Médicale (INSERM)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Université Bourgogne Franche-Comté [COMUE] (UBFC), Département d'Epilepsie, Sommeil et Neurophysiologie Pédiatrique [HCL, Lyon], Hospices Civils de Lyon (HCL), Institute of Human Genetics, University Hospital Magdeburg, Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Groupement hospitalier Lyon-Est, Centre de recherche en neurosciences de Lyon (CRNL), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), and CHU Toulouse [Toulouse]-Hôpital Purpan [Toulouse]
Subjects: Male, 0301 basic medicine, Proband, DEPDC5, SUDEP, 030105 genetics & heredity, Bioinformatics, Loss of Function Mutation/genetics, Epilepsy, INDEL Mutation, Loss of Function Mutation, mTORC1 pathway, Genetics(clinical), Child, Genetics (clinical), Multiprotein Complexes/genetics, Brugada Syndrome, DNA Copy Number Variation, Brugada syndrome, INDEL Mutation/genetics, GTPase-Activating Proteins, NPRL3, Seizure, Phenotype, Pedigree, 3. Good health, Brugada Syndrome/genetics, Child, Preschool, Female, Human, Signal Transduction, DNA Copy Number Variations, Adolescent, Seizures/complications, Mechanistic Target of Rapamycin Complex 1/genetics, DNA Copy Number Variations/genetics, Mechanistic Target of Rapamycin Complex 1, Tumor Suppressor Proteins/genetics, Article, Focal cortical dysplasia, 03 medical and health sciences, Seizures, GTPase-Activating Proteins/genetics, medicine, Humans, Genetic Predisposition to Disease, Genetic focal epilepsy, Epilepsy/complications, Repressor Proteins/genetics, business.industry, GTPase-Activating Protein, Tumor Suppressor Proteins, Infant, Newborn, Correction, Infant, Repressor Protein, Cortical dysplasia, medicine.disease, ddc:616.8, Repressor Proteins, 030104 developmental biology, Frontal lobe seizures, [SDV.GEN.GH]Life Sciences [q-bio]/Genetics/Human genetics, Multiprotein Complexes, Multiprotein Complexe, Signal Transduction/genetics, Human medicine, business
Abstract: Purpose:\ud \ud To define the phenotypic and mutational spectrum of epilepsies related to DEPDC5, NPRL2 and NPRL3 genes encoding the GATOR1 complex, a negative regulator of the mTORC1 pathway.\ud \ud Methods:\ud \ud We analyzed clinical and genetic data of 73 novel probands (familial and sporadic) with epilepsy-related variants in GATOR1-encoding genes and proposed new guidelines for clinical interpretation of GATOR1 variants.\ud \ud Results:\ud \ud The GATOR1 seizure phenotype consisted mostly in focal seizures (e.g., hypermotor or frontal lobe seizures in 50%), with a mean age at onset of 4.4 years, often sleep-related and drug-resistant (54%), and associated with focal cortical dysplasia (20%). Infantile spasms were reported in 10% of the probands. Sudden unexpected death in epilepsy (SUDEP) occurred in 10% of the families. Novel classification framework of all 140 epilepsy-related GATOR1 variants (including the variants of this study) revealed that 68% are loss-of-function pathogenic, 14% are likely pathogenic, 15% are variants of uncertain significance and 3% are likely benign.\ud \ud Conclusion:\ud \ud Our data emphasize the increasingly important role of GATOR1 genes in the pathogenesis of focal epilepsies (>180 probands to date). The GATOR1 phenotypic spectrum ranges from sporadic early-onset epilepsies with cognitive impairment comorbidities to familial focal epilepsies, and SUDEP.
Published: 2018
Full Text: View/download PDF

41. The neutral frequency spectrum of linked sites

Author: Emanuele Raineri, Thomas Wiehe, Guillaume Achaz, Alexander Klassmann, Luca Ferretti, Sebastian E. Ramos-Onsins, Agence Nationale de la Recherche (France), and German Research Foundation
Subjects: musculoskeletal diseases, 0301 basic medicine, 0106 biological sciences, Expected value, 010603 evolutionary biology, 01 natural sciences, Linkage Disequilibrium, Spectral line, Coalescent theory, Evolution, Molecular, 010104 statistics & probability, 03 medical and health sciences, fluids and secretions, Mutation Rate, Simple (abstract algebra), Quantitative Biology::Populations and Evolution, Statistical physics, Selection, Genetic, 0101 mathematics, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Physics, 0303 health sciences, Models, Genetic, Expression (mathematics), Genetics, Population, 030104 developmental biology, Mutation (genetic algorithm), Kolmogorov equations, Neutral theory of molecular evolution, Recombination
Abstract: bioRxiv, We introduce the conditional Site Frequency Spectrum (SFS) for a genomic region linked to a focal mutation of known frequency. An exact expression for its expected value is provided for the neutral model without recombination. Its relation with the expected SFS for two sites, 2-SFS, is discussed. These spectra derive from the coalescent approach of Fu (1995) for finite samples, which is reviewed. Remarkably simple expressions are obtained for the linked SFS of a large population, which are also solutions of the multi-allelic Kolmogorov equations. These formulae are the immediate extensions of the well known single site θ/f neutral SFS. Besides the general interest in these spectra, they relate to relevant biological cases, such as structural variants and introgressions. As an application, a recipe to adapt Tajima’s and other SFS-based neutrality tests to a non-recombining region containing a neutral marker is presented., GA and LF were supported by grant ANR-12-JSV7-0007 TempoMut from Agence Nationale de la Recherche. GA was also supported by grant ANR-12-BSV7-0012 Demochips, AK and TW by grants of the German Science Foundation (DFG-SFB680 and DFG-SPP 1590).
Published: 2018

42. Author response: Quiescence unveils a novel mutational force in fission yeast

Author: Benoit Arcangioli, Adrien Villain, Serge Gangloff, Guillaume Achaz, Claire Denis, Stefania Francesconi, and Samia Miled
Subjects: Chemistry, Fission, Yeast, Cell biology
Published: 2017
Full Text: View/download PDF

43. Coalescent Processes with Skewed Offspring Distributions and non-Equilibrium Demography

Author: Sebastian Matuszewski, Marcel E. Hildebrandt, Guillaume Achaz, and Jeffrey D. Jensen
Subjects: Linkage disequilibrium, education.field_of_study, Exponential growth, Reproductive success, Ecology (disciplines), Population, Inference, Quantitative Biology::Populations and Evolution, Variation (game tree), Biology, education, Coalescent theory, Demography
Abstract: Non-equilibrium demography impacts coalescent genealogies leaving detectable, well-studied signatures of variation. However, similar genomic footprints are also expected under models of large reproductive skew, posing a serious problem when trying to make inference. Furthermore, current approaches consider only one of the two processes at a time, neglecting any genomic signal that could arise from their simultaneous effects, preventing the possibility of jointly inferring parameters relating to both offspring distribution and population history. Here, we develop an extended Moran model with exponential population growth, and demonstrate that the underlying ancestral process converges to a time-inhomogeneous psi-coalescent. However, by applying a non-linear change of time scale -- analogous to the Kingman coalescent -- we find that the ancestral process can be rescaled to its time-homogeneous analogue, allowing the process to be simulated quickly and efficiently. Furthermore, we derive analytical expressions for the expected site-frequency spectrum under the time-inhomogeneous psi-coalescent and develop an approximate-likelihood framework for the joint estimation of the coalescent and growth parameters. By means of extensive simulation, we demonstrate that both can be estimated accurately given linkage equilibrium, while linkage disequilibrium systematically biases growth rate estimates. In addition, not accounting for demography can lead to serious biases in the inferred coalescent model, with broad implications for genomic studies ranging from ecology to conservation biology. Finally, we use our method to analyze sequence data from Japanese sardine populations and find evidence of high variation in individual reproductive success, but few signs of a recent demographic expansion.
Published: 2017
Full Text: View/download PDF

44. Coalescent Processes with Skewed Offspring Distributions and Nonequilibrium Demography

Author: Guillaume Achaz, Marcel Hildebrandt, Sebastian Matuszewski, and Jeffrey D. Jensen
Subjects: 0301 basic medicine, education.field_of_study, Reproductive success, Ecology (disciplines), Population, Skew, Inference, Variation (game tree), Biology, Models, Theoretical, Investigations, Coalescent theory, 03 medical and health sciences, 030104 developmental biology, Exponential growth, Genetics, Quantitative Biology::Populations and Evolution, education, Algorithms, Demography
Abstract: Nonequilibrium demography impacts coalescent genealogies leaving detectable, well-studied signatures of variation. However, similar genomic footprints are also expected under models of large reproductive skew, posing a serious problem when trying to make inference. Furthermore, current approaches consider only one of the two processes at a time, neglecting any genomic signal that could arise from their simultaneous effects, preventing the possibility of jointly inferring parameters relating to both offspring distribution and population history. Here, we develop an extended Moran model with exponential population growth, and demonstrate that the underlying ancestral process converges to a time-inhomogeneous psi-coalescent. However, by applying a nonlinear change of time scale—analogous to the Kingman coalescent—we find that the ancestral process can be rescaled to its time-homogeneous analog, allowing the process to be simulated quickly and efficiently. Furthermore, we derive analytical expressions for the expected site-frequency spectrum under the time-inhomogeneous psi-coalescent, and develop an approximate-likelihood framework for the joint estimation of the coalescent and growth parameters. By means of extensive simulation, we demonstrate that both can be estimated accurately from whole-genome data. In addition, not accounting for demography can lead to serious biases in the inferred coalescent model, with broad implications for genomic studies ranging from ecology to conservation biology. Finally, we use our method to analyze sequence data from Japanese sardine populations, and find evidence of high variation in individual reproductive success, but few signs of a recent demographic expansion.
Published: 2017

45. Quiescence unveils a novel mutational force in fission yeast

Author: Samia Miled, Benoit Arcangioli, Adrien Villain, Serge Gangloff, Guillaume Achaz, and Claire Denis
Subjects: Genetics, 0303 health sciences, Natural selection, Cell division, DNA replication, Genomics, Biology, Phenotype, Genome, Yeast, 03 medical and health sciences, 0302 clinical medicine, Ploidy, 030217 neurology & neurosurgery, 030304 developmental biology
Abstract: One Sentence SummaryThe quiescence-driven mutational landscape reveals a novel evolutionary force.AbstractDuring cell division, the spontaneous mutation rate is expressed as the probability of mutations per generation, whereas during quiescence it will be expressed per unit of time. In this study, we report that during quiescence, the unicellular haploid fission yeast accumulates mutations as a linear function of time. We determined that 3 days of quiescence generate a number of invalidating mutations equivalent to that of one round of DNA replication. The novel mutational landscape of quiescence is characterized by insertion/deletion accumulating as fast as single nucleotide variants, and elevated amounts of deletions. When we extended the study to 3 months of quiescence, we confirmed the replication-independent mutational spectrum at the whole-genome level of a clonally aged population and uncovered phenotypic variations that subject the cells to natural selection. Thus, our results support the idea that genomes continuously evolve under two alternating phases that will impact on their size and composition.
Published: 2017
Full Text: View/download PDF

46. Yeast de novo genes preferentially emerge from divergently transcribed, GC-rich intergenic regions

Author: Vakirlis N N, Alexander S. Hebert, Joshua J. Coon, Dana A. Opulente, Ingrid Lafontaine, Gilles Fischer, Guillaume Achaz, and Chris Todd Hittinger
Subjects: Genetics, 0303 health sciences, Promoter, Translation (biology), Biology, Genome, Yeast, 03 medical and health sciences, 0302 clinical medicine, Intergenic region, Phylogenetics, Homologous chromosome, Gene, 030217 neurology & neurosurgery, 030304 developmental biology
Abstract: New genes, with novel protein functions, can evolve “from scratch” out of intergenic sequences. These de novo genes can integrate the cell’s genetic network and drive important phenotypic innovations. Therefore, identifying de novo genes and understanding how the transition from noncoding to coding occurs are key problems in evolutionary biology. However, identifying de novo genes is a difficult task, hampered by the presence of remote homologs, fast evolving sequences and erroneously annotated protein coding genes. To overcome these limitations, we developed a procedure that handles the usual pitfalls in de novo gene identification and predicted the emergence of 703 de novo genes in 15 yeast species from two genera whose phylogeny spans at least 100 million years of evolution. We established that de novo gene origination is a widespread phenomenon in yeasts, only a few being ultimately maintained by selection. We validated 82 candidates, by providing new translation evidence for 25 of them through mass spectrometry experiments. We also unambiguously identified the mutations that enabled the transition from non-coding to coding for 30 Saccharomyces de novo genes. We found that de novo genes preferentially emerge next to divergent promoters in GC-rich intergenic regions where the probability of finding a fortuitous and transcribed ORF is the highest. We found a more than 3-fold enrichment of de novo genes at recombination hot spots, which are GC-rich and nucleosome-free regions, suggesting that meiotic recombination would be a major driving force of de novo gene emergence in yeasts.
Published: 2017
Full Text: View/download PDF

47. Properties of selected mutations and genotypic landscapes under Fisher's geometric model

Author: François Blanquart, Guillaume Achaz, Thomas Bataillon, and Olivier Tenaillon
Subjects: 0106 biological sciences, Genetics, 0303 health sciences, Neutral network, Fitness landscape, Genetic Fitness, Biology, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, NK model, Evolutionary biology, Fisher's geometric model, Epistasis, Adaptation, General Agricultural and Biological Sciences, Ecology, Evolution, Behavior and Systematics, Selection (genetic algorithm), 030304 developmental biology
Abstract: The fitness landscape – the mapping between genotypes and fitness – determines properties of the process of adaptation. Several small genotypic fitness landscapes have recently been built by selecting a handful of beneficial mutations and measuring fitness of all combinations of these mutations. Here we generate several testable predictions for the properties of these small genotypic landscapes under Fisher’s geometric model of adaptation. When the ancestral strain is far from the fitness optimum, we analytically compute the fitness effect of selected mutations and their epistatic interactions. Epistasis may be negative or positive on average depending on the distance of the ancestral genotype to the optimum and whether mutations were independently selected, or co-selected in an adaptive walk. Simulations show that genotypic landscapes built from Fisher’s model are very close to an additive landscape when the ancestral strain is far from the optimum. However, when it is close to the optimum, a large diversity of landscape with substantial roughness and sign epistasis emerged. Strikingly, small genotypic landscapes built from several replicate adaptive walks on the same underlying landscape were highly variable, suggesting that several realizations of small genotypic landscapes are needed to gain information about the underlying architecture of the fitness landscape.
Published: 2014
Full Text: View/download PDF

48. Accuracy of demographic inferences from site frequency spectrum: the case of the yoruba population

Author: Guillaume Achaz, Amaury Lambert, and Marguerite Lapierre
Subjects: education.field_of_study, Computer science, Population, Yoruba, Inference, Overfitting, Summary statistics, language.human_language, Statistics, language, Piecewise, Population growth, 1000 Genomes Project, education
Abstract: Some methods for demographic inference based on the observed genetic diversity of current populations rely on the use of summary statistics such as the Site Frequency Spectrum (SFS). Demographic models can be either model-constrained with numerous parameters such as growth rates, timing of demographic events and migration rates, or model-flexible, with an unbounded collection of piecewise constant sizes. It is still debated whether demographic histories can be accurately inferred based on the SFS. Here we illustrate this theoretical issue on an example of demographic inference for an African population. The SFS of the Yoruba population (data from the 1000 Genomes Project) is fit to a simple model of population growth described with a single parameter (e.g., founding time). We infer a time to the most recent common ancestor of 1.7 million years for this population. However, we show that the Yoruba SFS is not informative enough to discriminate between several different models of growth. We also show that for such simple demographies, the fit of one-parameter models outperforms the model-flexible method recently developed by Liu and Fu. The use of this method on simulated data suggests that it is biased by the noise intrinsically present in the data.
Published: 2016
Full Text: View/download PDF

49. Testing for independence between evolutionary processes

Author: Guillaume Achaz, Joël Pothier, Abdelkader Behdenna, Sophie S. Abby, Amaury Lambert, Adaptation aux milieux extrêmes, Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Atelier de BioInformatique (ABI), Université Pierre et Marie Curie - Paris 6 (UPMC), Génomique évolutive des Microbes / Microbial Evolutionary Genomics, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Systématique, adaptation, évolution (SAE), Centre interdisciplinaire de recherche en biologie (CIRB), Labex MemoLife, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-Collège de France (CdF (institution))-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Collège de France (CdF (institution))-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM), Laboratoire de Probabilités et Modèles Aléatoires (LPMA), Centre National de la Recherche Scientifique (CNRS)-Université Paris Diderot - Paris 7 (UPD7)-Université Pierre et Marie Curie - Paris 6 (UPMC), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Collège de France (CdF (institution))-Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), and Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, Biology, phylogeny, 03 medical and health sciences, 0302 clinical medicine, statistal test, Genetics, Computer Simulation, Ecology, Evolution, Behavior and Systematics, Independence (probability theory), Probability, Statistical hypothesis testing, Event (probability theory), Phylogenetic tree, Null model, Classification, Biological Evolution, [MATH.MATH-PR]Mathematics [math]/Probability [math.PR], Tree (data structure), 030104 developmental biology, Data Interpretation, Statistical, coevolution, Epistasis, Probability distribution, Algorithm, 030217 neurology & neurosurgery
Abstract: International audience; Evolutionary events co-occurring along phylogenetic trees usually point to complex adaptive phenomena, sometimes implicating epistasis. While a number of methods have been developed to account for co-occurrence of events on the same internal or external branch of an evolutionary tree, there is a need to account for the larger diversity of possible relative positions of events in a tree. Here we propose a method to quantify to what extent two or more evolutionary events are associated on a phylogenetic tree. The method is applicable to any discrete character, like substitutions within a coding sequence or gains/losses of a biological function. Our method uses a general approach to statistically test for significant associations between events along the tree, which encompasses both events inseparable on the same branch, and events genealogically ordered on different branches. It assumes that the phylogeny and themapping of branches is known without errors. We address this problem from the statistical viewpoint by a linear algebra representation of the localization of the evolutionary events on the tree.We compute the full probability distribution of the number of paired events occurring in the same branch or in different branches of the tree, under a null model of independence where each type of event occurs at a constant rate uniformly inthephylogenetic tree. The strengths andweaknesses of themethodare assessed via simulations;we then apply the method to explore the loss of cell motility in intracellular pathogens.
Published: 2016
Full Text: View/download PDF

50. MicNeSs: genotyping microsatellite loci from a collection of (NGS) reads

Author: Marie Suez, Sophie Brouillet, Paula Graça, Dominique Higuet, Guillaume Achaz, Abdelkader Behdenna, Evolution des Génomes Eucaryotes (EGE), Evolution Paris Seine, Université des Antilles et de la Guyane (UAG)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles et de la Guyane (UAG)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS), Cofiroute and the Parc Naturel Regional de la Haute Vallee de Chevreuse, Demochips from the Agence Nationale de la Recherche (France) [ANR-12-BSV7-0012], Université des Antilles et de la Guyane (UAG)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Nice Sophia Antipolis (1965 - 2019) (UNS), and COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles et de la Guyane (UAG)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Nice Sophia Antipolis (1965 - 2019) (UNS)
Subjects: 0301 basic medicine, Genetics, Genotyping Techniques, Population genetics, Computational Biology, High-Throughput Nucleotide Sequencing, Locus (genetics), Computational biology, [SDV.BID]Life Sciences [q-bio]/Biodiversity, Biology, microsatellite loci, 03 medical and health sciences, 030104 developmental biology, genotyping, Genotype, Microsatellite, Pyrosequencing, Allele, next-generation sequencing (NGS), Genotyping, Ecology, Evolution, Behavior and Systematics, Biotechnology, Microsatellite Repeats
Abstract: International audience; Microsatellites are widely used in population genetics to uncover recent evolutionary events. They are typically genotyped using capillary sequencer, which capacity is usually limited to 9, at most 12 loci for each run, and which analysis is a tedious task that is performed by hand. With the rise of next-generation sequencing (NGS), a much larger number of loci and individuals are available from sequencing: for example, on a single run of a GS Junior, 28 loci from 96 individuals are sequenced with a 30X cover. We have developed an algorithm to automatically and efficiently genotype microsatellites from a collection of reads sorted by individual (e.g. specific PCR amplifications of a locus or a collection of reads that encompass a locus of interest). As the sequencing and the PCR amplification introduce artefactual insertions or deletions, the set of reads from a single microsatellite allele shows several length variants. The algorithm infers, without alignment, the true unknown allele(s) of each individual from the observed distributions of microsatellites length of all individuals. MicNeSs, a python implementation of the algorithm, can be used to genotype any microsatellite locus from any organism and has been tested on 454 pyrosequencing data of several loci from fruit flies (a model species) and red deers (a nonmodel species). Without any parallelization, it automatically genotypes 22 loci from 441 individuals in 11 hours on a standard computer. The comparison of MicNeSs inferences to the standard method shows an excellent agreement, with some differences illustrating the pros and cons of both methods.
Published: 2016
Full Text: View/download PDF

Catalog

Books, media, physical & digital resources

See catalog results

Searchworks

Select search scope, currently: Articles Catalog books, media & more in Jio Institute collections Articles journal articles & other e-resources

Search

Search Constraints

Refine your results

Search Limiters

Topic

Publication Year Range

Language

Publication Type

Journal

Database

Publisher

89 results on '"Guillaume Achaz"'

Search Results

Catalog

Select search scope, currently: Articles

Catalog

books, media & more in Jio Institute collections

Articles

journal articles & other e-resources